nf-core · ewels · May 10, 2021 · May 10, 2021 · May 10, 2021 · May 10, 2021
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -31,6 +31,7 @@
 * Fix overly strict `--max_time` formatting regex in template schema [[#973](https://github.com/nf-core/tools/issues/973)]
 * Added `tool_name_underscore` to the module template to allow TOOL_SUBTOOL in `main.nf` [[#1011](https://github.com/nf-core/tools/issues/1011)]
 * Convert `d` to `day` in the `cleanParameters` function to make Duration objects like `2d` pass the validation [[#858](https://github.com/nf-core/tools/issues/858)]
+* Added nextflow version to quick start section and adjusted `nf-core bump-version` [[#1032](https://github.com/nf-core/tools/issues/1032)]
 
 ## [v1.13.3 - Copper Crocodile Resurrection :crocodile:](https://github.com/nf-core/tools/releases/tag/1.13.2) - [2021-03-24]
 

diff --git a/nf_core/bump_version.py b/nf_core/bump_version.py
@@ -145,7 +145,8 @@ def bump_nextflow_version(pipeline_obj, new_version):
         pipeline_obj,
         [
             (
-                r"nxf_ver: \[[\'\"]?{}[\'\"]?, ''\]".format(current_version.replace(".", r"\.")),
+                # example: nxf_ver: ['20.04.0', '']
+                r"nxf_ver: \[[\'\"]{}[\'\"], [\'\"][\'\"]\]".format(current_version.replace(".", r"\.")),
                 "nxf_ver: ['{}', '']".format(new_version),
             )
         ],
@@ -159,7 +160,14 @@ def bump_nextflow_version(pipeline_obj, new_version):
             (
                 r"nextflow-%E2%89%A5{}-brightgreen.svg".format(current_version.replace(".", r"\.")),
                 "nextflow-%E2%89%A5{}-brightgreen.svg".format(new_version),
-            )
+            ),
+            (
+                # example: 1. Install [`nextflow`](https://nf-co.re/usage/installation) (`>=20.04.0`)
+                r"1\.\s*Install\s*\[`nextflow`\]\(https://nf-co\.re/usage/installation\)\s*\(`>={}`\)".format(
+                    current_version.replace(".", r"\.")
+                ),
+                "1. Install [`nextflow`](https://nf-co.re/usage/installation) (`>={}`)".format(new_version),
+            ),
         ],
     )
 
@@ -190,24 +198,36 @@ def update_file_version(filename, pipeline_obj, patterns):
     replacements = []
     for pattern in patterns:
 
-        # Check that we have a match
-        matches_pattern = re.findall("^.*{}.*$".format(pattern[0]), content, re.MULTILINE)
-        if len(matches_pattern) == 0:
-            log.error("Could not find version number in {}: '{}'".format(filename, pattern))
-            continue
+        found_match = False
 
-        # Replace the match
-        content = re.sub(pattern[0], pattern[1], content)
-        matches_newstr = re.findall("^.*{}.*$".format(pattern[1]), content, re.MULTILINE)
+        newcontent = []
+        for line in content.splitlines():
 
-        # Save for logging
-        replacements.append((matches_pattern, matches_newstr))
+            # Match the pattern
+            matches_pattern = re.findall("^.*{}.*$".format(pattern[0]), line)
+            if matches_pattern:
+                found_match = True
+
+                # Replace the match
+                newline = re.sub(pattern[0], pattern[1], line)
+                newcontent.append(newline)
+
+                # Save for logging
+                replacements.append((line, newline))
+
+            # No match, keep line as it is
+            else:
+                newcontent.append(line)
+
+        if found_match:
+            content = "\n".join(newcontent)
+        else:
+            log.error("Could not find version number in {}: '{}'".format(filename, pattern))
 
     log.info("Updated version in '{}'".format(filename))
     for replacement in replacements:
-        for idx, matched in enumerate(replacement[0]):
-            stderr.print("          [red] - {}".format(matched.strip()), highlight=False)
-            stderr.print("          [green] + {}".format(replacement[1][idx].strip()), highlight=False)
+        stderr.print("          [red] - {}".format(replacement[0].strip()), highlight=False)
+        stderr.print("          [green] + {}".format(replacement[1].strip()), highlight=False)
     stderr.print("\n")
 
     with open(fn, "w") as fh:

diff --git a/nf_core/pipeline-template/README.md b/nf_core/pipeline-template/README.md
@@ -19,7 +19,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool
 
 ## Quick Start
 
-1. Install [`nextflow`](https://nf-co.re/usage/installation)
+1. Install [`nextflow`](https://nf-co.re/usage/installation) (`>=21.04.0`)
 
 2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(please only use [`Conda`](https://conda.io/miniconda.html) as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_